The software currently takes as input FASTA-formatted genomic sequences, GTF-formatted transcript annotations and FASTQ-formatted RNA-Seq data.
The chapter is formatted like a transcript, and Rosie, a good talk-show guest, gets philosophical: "Life is short.
To detect and annotate AS events in a user-submitted transcript (termed 'query transcript'), AS-EAST accepts a FASTA-formatted transcript sequence.
Qualitative interview transcripts were formatted and imported into NVivo 10 [QSR International, Australia] for data management, coding and analysis.
The complete annotation and sequence information comprising: Gene structure releases in GFF3 format: gene, transcript, CDS, protein, UTR sequences in FASTA format; Mappings/lookup tables, GO annotations in GAF format are accessible via the cosmoss.org download section [ 122].
Gene models, transcript sequences, microarray expression data and gene network data were stored in the MySQL database, and transcript sequences were formatted as a Basic Local Alignment Search Tool BLASTT) database.
A more complete format for transcript quantification is known as solution hybridization, epitomized in the form of the nuclease protection assays and, of course, the polymerase chain reaction.
Badger accepts gene set data (GFF3 format) with corresponding transcript and protein sequences (FASTA format), and also data in BLAST XML output, InterProScan raw output and Tab Separated Value (TSV) custom annotation files.
I took the notes of the meeting, in transcript format, that were so detailed and accurate that the senators testified that they were sure I had tape recorded the meeting.
